1
|
Liu Q, Peng Q, Zhang B, Tan Y. X-ray cross-complementing family: the bridge linking DNA damage repair and cancer. J Transl Med 2023; 21:602. [PMID: 37679817 PMCID: PMC10483876 DOI: 10.1186/s12967-023-04447-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 08/17/2023] [Indexed: 09/09/2023] Open
Abstract
Genomic instability is a common hallmark of human tumours. As a carrier of genetic information, DNA is constantly threatened by various damaging factors that, if not repaired in time, can affect the transmission of genetic information and lead to cellular carcinogenesis. In response to these threats, cells have evolved a range of DNA damage response mechanisms, including DNA damage repair, to maintain genomic stability. The X-ray repair cross-complementary gene family (XRCC) comprises an important class of DNA damage repair genes that encode proteins that play important roles in DNA single-strand breakage and DNA base damage repair. The dysfunction of the XRCC gene family is associated with the development of various tumours. In the context of tumours, mutations in XRCC and its aberrant expression, result in abnormal DNA damage repair, thus contributing to the malignant progression of tumour cells. In this review, we summarise the significant roles played by XRCC in diverse tumour types. In addition, we discuss the correlation between the XRCC family members and tumour therapeutic sensitivity.
Collapse
Affiliation(s)
- Qiang Liu
- Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 283 Tongzipo Road, Changsha, 410013, Hunan, China
- NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Sciences, Institute of Reproductive and Stem Cell Engineering, Central South University, Changsha, 410078, Hunan, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, 410008, Hunan, China
| | - Qiu Peng
- Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 283 Tongzipo Road, Changsha, 410013, Hunan, China
| | - Bin Zhang
- Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 283 Tongzipo Road, Changsha, 410013, Hunan, China.
- Department of Histology and Embryology, Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China.
| | - Yueqiu Tan
- Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 283 Tongzipo Road, Changsha, 410013, Hunan, China.
- NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Sciences, Institute of Reproductive and Stem Cell Engineering, Central South University, Changsha, 410078, Hunan, China.
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, 410008, Hunan, China.
| |
Collapse
|
2
|
Brewer T, Yehia L, Bazeley P, Eng C. Integrating somatic CNV and gene expression in breast cancers from women with PTEN hamartoma tumor syndrome. NPJ Genom Med 2023; 8:14. [PMID: 37407629 DOI: 10.1038/s41525-023-00361-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 06/14/2023] [Indexed: 07/07/2023] Open
Abstract
Women with germline PTEN variants (PTEN hamartoma tumor syndrome, PHTS) have up to 85% lifetime risk of female breast cancer (BC). We previously showed that PHTS-derived BCs are distinct from sporadic BCs both at the clinical and genomic levels. In this study, we examined somatic copy number variations (CNV) and transcriptome data to further characterize the somatic landscape of PHTS-derived BCs. We analyzed exome sequencing data from 44 BCs from women with PHTS for CNV. The control group comprised of 558 women with sporadic BCs from The Cancer Genome Atlas (TCGA) dataset. Here, we found that PHTS-derived BCs have several distinct CNV peaks compared to TCGA. Furthermore, RNA sequencing data revealed that PHTS-derived BCs have a distinct immunologic cell type signature, which points toward cancer immune evasion. Transcriptomic data also revealed PHTS-derived BCs with pathogenic germline PTEN variants appear to have vitamin E degradation as a key pathway associated with tumorigenesis. In conclusion, our study revealed distinct CNV x transcript features in PHTS-derived BCs, which further facilitate understanding of BC biology arising in the setting of germline PTEN mutations.
Collapse
Affiliation(s)
- Takae Brewer
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH, 44195, USA
| | - Lamis Yehia
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Peter Bazeley
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Charis Eng
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA.
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH, 44195, USA.
- Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, 44195, USA.
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA.
- Germline High Risk Cancer Focus Group, Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, 44106, USA.
| |
Collapse
|
3
|
Bilyalov A, Nikolaev S, Shigapova L, Khatkov I, Danishevich A, Zhukova L, Smolin S, Titova M, Lisica T, Bodunova N, Shagimardanova E, Gusev O. Application of Multigene Panels Testing for Hereditary Cancer Syndromes. BIOLOGY 2022; 11:biology11101461. [PMID: 36290365 PMCID: PMC9598138 DOI: 10.3390/biology11101461] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 09/28/2022] [Accepted: 09/30/2022] [Indexed: 11/06/2022]
Abstract
BACKGROUND Approximately 5-10% of all cancers are associated with hereditary cancer predisposition syndromes (HCPS). Early identification of HCPS is facilitated by widespread use of next-generation sequencing (NGS) and brings significant benefits to both the patient and their relatives. This study aims to evaluate the landscape of genetic variants in patients with personal and/or family history of cancer using NGS-based multigene panel testing. MATERIALS AND METHODS The study cohort included 1117 probands from Russia: 1060 (94.9%) patients with clinical signs of HCPS and 57 (5.1%) healthy individuals with family history of cancer. NGS analysis of 76 HCPS genes was performed using a custom Roche NimbleGen enrichment panel. RESULTS Pathogenic/likely pathogenic variants were identified in 378 of 1117 individuals (33.8%). The predominant number (59.8%) of genetic variants was identified in BRCA1/BRCA2 genes. CHEK2 was the second most commonly altered gene with a total of 28 (7.4%) variants, and 124 (32.8%) genetic variants were found in other 35 cancer-associated genes with variable penetrance. CONCLUSIONS Multigene panel testing allows for a differential diagnosis and identification of high-risk group for oncological diseases. Our results demonstrate that inclusion of non-coding gene regions into HCPS gene panels is highly important for the identification of rare spliceogenic variants with high penetrance.
Collapse
Affiliation(s)
- Airat Bilyalov
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia
- The Loginov Moscow Clinical Scientific Center, 111123 Moscow, Russia
- Correspondence: ; Tel.: +7-9625-6038-02
| | - Sergey Nikolaev
- The Loginov Moscow Clinical Scientific Center, 111123 Moscow, Russia
| | - Leila Shigapova
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia
| | - Igor Khatkov
- The Loginov Moscow Clinical Scientific Center, 111123 Moscow, Russia
| | | | - Ludmila Zhukova
- The Loginov Moscow Clinical Scientific Center, 111123 Moscow, Russia
| | - Sergei Smolin
- The Loginov Moscow Clinical Scientific Center, 111123 Moscow, Russia
| | - Marina Titova
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia
| | - Tatyana Lisica
- Centre for Strategic Planning of FMBA of Russia, 119121 Moscow, Russia
| | - Natalia Bodunova
- The Loginov Moscow Clinical Scientific Center, 111123 Moscow, Russia
| | - Elena Shagimardanova
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia
| | - Oleg Gusev
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia
- Graduate School of Medicine, Juntendo University, Tokyo 113-8421, Japan
- Endocrinology Research Centre, 117036 Moscow, Russia
| |
Collapse
|
4
|
Brewer T, Yehia L, Bazeley P, Eng C. Exome sequencing reveals a distinct somatic genomic landscape in breast cancer from women with germline PTEN variants. Am J Hum Genet 2022; 109:1520-1533. [PMID: 35931053 PMCID: PMC9388380 DOI: 10.1016/j.ajhg.2022.07.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 07/01/2022] [Indexed: 02/06/2023] Open
Abstract
Germline PTEN variants (PTEN hamartoma tumor syndrome [PHTS]) confer up to 85% lifetime risk of female breast cancer (BC). BCs arising in PHTS are clinically distinct from sporadic BCs, including younger age of onset, multifocality, and an increased risk of second primary BCs. Yet, there is no previous investigation into the underlying genomic landscape of this entity. We sought to address the hypothesis that BCs arising in PHTS have a distinct genomic landscape compared to sporadic counterparts. We performed and analyzed exome sequencing data from 44 women with germline PTEN variants who developed BCs. The control cohort comprised of 497 women with sporadic BCs from The Cancer Genome Atlas (TCGA) dataset. We demonstrate that PHTS-derived BCs have a distinct somatic mutational landscape compared to the sporadic counterparts, namely second somatic hits in PTEN, distinct mutational signatures, and increased genomic instability. The PHTS group had a significantly higher frequency of somatic PTEN variants compared to TCGA (22.7% versus 5.6%; odds ratio [OR] 4.93; 95% confidence interval [CI] 2.21 to 10.98; p < 0.001) and a lower mutational frequency in PIK3CA (22.7% versus 33.4%; OR 0.59; 95% CI 0.28 to 1.22; p = 0.15). Somatic variants in PTEN and PIK3CA were mutually exclusive in PHTS (p = 0.01) but not in TCGA. Our findings have important implications for the personalized management of PTEN-related BCs, especially in the context of more accessible genetic testing.
Collapse
Affiliation(s)
- Takae Brewer
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA,Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH 44195, USA
| | - Lamis Yehia
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Peter Bazeley
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Charis Eng
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA,Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH 44195, USA,Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH 44195, USA,Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA,Germline High Risk Cancer Focus Group, Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106, USA,Corresponding author
| |
Collapse
|
5
|
Badra Fajardo N, Taraviras S, Lygerou Z. Fanconi anemia proteins and genome fragility: unraveling replication defects for cancer therapy. Trends Cancer 2022; 8:467-481. [DOI: 10.1016/j.trecan.2022.01.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 01/25/2022] [Indexed: 10/19/2022]
|
6
|
Almansour NM. Triple-Negative Breast Cancer: A Brief Review About Epidemiology, Risk Factors, Signaling Pathways, Treatment and Role of Artificial Intelligence. Front Mol Biosci 2022; 9:836417. [PMID: 35145999 PMCID: PMC8824427 DOI: 10.3389/fmolb.2022.836417] [Citation(s) in RCA: 114] [Impact Index Per Article: 57.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 01/07/2022] [Indexed: 12/12/2022] Open
Abstract
Triple-negative breast cancer (TNBC) is a kind of breast cancer that lacks estrogen, progesterone, and human epidermal growth factor receptor 2. This cancer is responsible for more than 15-20% of all breast cancers and is of particular research interest as it is therapeutically challenging mainly because of its low response to therapeutics and highly invasive nature. The non-availability of specific treatment options for TNBC is usually managed by conventional therapy, which often leads to relapse. The focus of this review is to provide up-to-date information related to TNBC epidemiology, risk factors, metastasis, different signaling pathways, and the pathways that can be blocked, immune suppressive cells of the TNBC microenvironment, current and investigation therapies, prognosis, and the role of artificial intelligence in TNBC diagnosis. The data presented in this paper may be helpful for researchers working in the field to obtain general and particular information to advance the understanding of TNBC and provide suitable disease management in the future.
Collapse
Affiliation(s)
- Nahlah Makki Almansour
- Department of Biology, College of Science, University of Hafr Al Batin, Hafr Al Batin, Saudi Arabia
| |
Collapse
|
7
|
Toh M, Ngeow J. Homologous Recombination Deficiency: Cancer Predispositions and Treatment Implications. Oncologist 2021; 26:e1526-e1537. [PMID: 34021944 PMCID: PMC8417864 DOI: 10.1002/onco.13829] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 12/03/2020] [Indexed: 12/19/2022] Open
Abstract
Homologous recombination (HR) is a highly accurate DNA repair mechanism. Several HR genes are established cancer susceptibility genes with clinically actionable pathogenic variants (PVs). Classically, BRCA1 and BRCA2 germline PVs are associated with significant breast and ovarian cancer risks. Patients with BRCA1 or BRCA2 PVs display worse clinical outcomes but respond better to platinum-based chemotherapies and poly-ADP ribose polymerase inhibitors, a trait termed "BRCAness." With the advent of whole-exome sequencing and multigene panels, PVs in other HR genes are increasingly identified among familial cancers. As such, several genes such as PALB2 are reclassified as cancer predisposition genes. But evidence for cancer risks remains unclear for many others. In this review, we will discuss cancer predispositions and treatment implications beyond BRCA1 and BRCA2, with a focus on 24 HR genes: 53BP1, ATM, ATR, ATRIP, BARD1, BLM, BRIP1, DMC1, MRE11A, NBN, PALB2, RAD50, RAD51, RAD51B, RAD51C, RAD51D, RIF1, RMI1, RMI2, RPA1, TOP3A, TOPBP1, XRCC2, and XRCC3. IMPLICATIONS FOR PRACTICE: This review provides a comprehensive reference for readers to quickly identify potential cancer predisposing homologous recombination (HR) genes, and to generate research questions for genes with inconclusive evidence. This review also evaluates the "BRCAness" of each HR member. Clinicians can refer to these discussions to identify potential candidates for future clinical trials.
Collapse
Affiliation(s)
- MingRen Toh
- Duke–National University of Singapore Medical SchoolSingapore
| | - Joanne Ngeow
- Cancer Genetics Service, Division of Medical Oncology, National Cancer CenterSingapore
- Lee Kong Chian School of Medicine, Nanyang Technological UniversitySingapore
| |
Collapse
|
8
|
Łukasiewicz S, Czeczelewski M, Forma A, Baj J, Sitarz R, Stanisławek A. Breast Cancer-Epidemiology, Risk Factors, Classification, Prognostic Markers, and Current Treatment Strategies-An Updated Review. Cancers (Basel) 2021; 13:cancers13174287. [PMID: 34503097 PMCID: PMC8428369 DOI: 10.3390/cancers13174287] [Citation(s) in RCA: 454] [Impact Index Per Article: 151.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 08/19/2021] [Accepted: 08/23/2021] [Indexed: 02/07/2023] Open
Abstract
Simple Summary Breast cancer is the most common cancer among women. It is estimated that 2.3 million new cases of BC are diagnosed globally each year. Based on mRNA gene expression levels, BC can be divided into molecular subtypes that provide insights into new treatment strategies and patient stratifications that impact the management of BC patients. This review addresses the overview on the BC epidemiology, risk factors, classification with an emphasis on molecular types, prognostic biomarkers, as well as possible treatment modalities. Abstract Breast cancer (BC) is the most frequently diagnosed cancer in women worldwide with more than 2 million new cases in 2020. Its incidence and death rates have increased over the last three decades due to the change in risk factor profiles, better cancer registration, and cancer detection. The number of risk factors of BC is significant and includes both the modifiable factors and non-modifiable factors. Currently, about 80% of patients with BC are individuals aged >50. Survival depends on both stage and molecular subtype. Invasive BCs comprise wide spectrum tumors that show a variation concerning their clinical presentation, behavior, and morphology. Based on mRNA gene expression levels, BC can be divided into molecular subtypes (Luminal A, Luminal B, HER2-enriched, and basal-like). The molecular subtypes provide insights into new treatment strategies and patient stratifications that impact the management of BC patients. The eighth edition of TNM classification outlines a new staging system for BC that, in addition to anatomical features, acknowledges biological factors. Treatment of breast cancer is complex and involves a combination of different modalities including surgery, radiotherapy, chemotherapy, hormonal therapy, or biological therapies delivered in diverse sequences.
Collapse
Affiliation(s)
- Sergiusz Łukasiewicz
- Department of Surgical Oncology, Center of Oncology of the Lublin Region St. Jana z Dukli, 20-091 Lublin, Poland; (S.Ł.); (A.S.)
| | - Marcin Czeczelewski
- Department of Forensic Medicine, Medical University of Lublin, 20-090 Lublin, Poland; (M.C.); (A.F.)
| | - Alicja Forma
- Department of Forensic Medicine, Medical University of Lublin, 20-090 Lublin, Poland; (M.C.); (A.F.)
| | - Jacek Baj
- Department of Human Anatomy, Medical University of Lublin, 20-090 Lublin, Poland;
| | - Robert Sitarz
- Department of Surgical Oncology, Center of Oncology of the Lublin Region St. Jana z Dukli, 20-091 Lublin, Poland; (S.Ł.); (A.S.)
- Department of Human Anatomy, Medical University of Lublin, 20-090 Lublin, Poland;
- Correspondence:
| | - Andrzej Stanisławek
- Department of Surgical Oncology, Center of Oncology of the Lublin Region St. Jana z Dukli, 20-091 Lublin, Poland; (S.Ł.); (A.S.)
- Department of Oncology, Chair of Oncology and Environmental Health, Medical University of Lublin, 20-081 Lublin, Poland
| |
Collapse
|
9
|
Gianni P, Matenoglou E, Geropoulos G, Agrawal N, Adnani H, Zafeiropoulos S, Miyara SJ, Guevara S, Mumford JM, Molmenti EP, Giannis D. The Fanconi anemia pathway and Breast Cancer: A comprehensive review of clinical data. Clin Breast Cancer 2021; 22:10-25. [PMID: 34489172 DOI: 10.1016/j.clbc.2021.08.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 07/17/2021] [Accepted: 08/05/2021] [Indexed: 02/08/2023]
Abstract
The development of breast cancer depends on several risk factors, including environmental, lifestyle and genetic factors. Despite the evolution of DNA sequencing techniques and biomarker detection, the epidemiology and mechanisms of various breast cancer susceptibility genes have not been elucidated yet. Dysregulation of the DNA damage response causes genomic instability and increases the rate of mutagenesis and the risk of carcinogenesis. The Fanconi Anemia (FA) pathway is an important component of the DNA damage response and plays a critical role in the repair of DNA interstrand crosslinks and genomic stability. The FA pathway involves 22 recognized genes and specific mutations have been identified as the underlying defect in the majority of FA patients. A thorough understanding of the function and epidemiology of these genes in breast cancer is critical for the development and implementation of individualized therapies that target unique tumor profiles. Targeted therapies (PARP inhibitors) exploiting the FA pathway gene defects have been developed and have shown promising results. This narrative review summarizes the current literature on the involvement of FA genes in sporadic and familial breast cancer with a focus on clinical data derived from large cohorts.
Collapse
Affiliation(s)
- Panagiota Gianni
- Department of Internal Medicine III, Hematology, Oncology, Palliative Medicine, Rheumatology and Infectious Diseases, University Hospital Ulm, Germany
| | - Evangelia Matenoglou
- Medical School, Aristotle University of Thessaloniki, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Georgios Geropoulos
- Thoracic Surgery Department, University College London Hospitals NHS Foundation Trust, London
| | - Nirav Agrawal
- Feinstein Institutes for Medical Research at Northwell Health, Manhasset, New York, NY
| | - Harsha Adnani
- Feinstein Institutes for Medical Research at Northwell Health, Manhasset, New York, NY
| | - Stefanos Zafeiropoulos
- Feinstein Institutes for Medical Research at Northwell Health, Manhasset, New York, NY; Elmezzi Graduate School of Molecular Medicine, Northwell Health, Manhasset, New York, NY
| | - Santiago J Miyara
- Feinstein Institutes for Medical Research at Northwell Health, Manhasset, New York, NY; Elmezzi Graduate School of Molecular Medicine, Northwell Health, Manhasset, New York, NY
| | - Sara Guevara
- Department of Surgery, North Shore University Hospital, Manhasset, New York, NY
| | - James M Mumford
- Department of Family Medicine, Glen Cove Hospital, Glen Cove, New York, NY; Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, New York, NY
| | - Ernesto P Molmenti
- Feinstein Institutes for Medical Research at Northwell Health, Manhasset, New York, NY; Department of Surgery, North Shore University Hospital, Manhasset, New York, NY; Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, New York, NY
| | - Dimitrios Giannis
- Feinstein Institutes for Medical Research at Northwell Health, Manhasset, New York, NY.
| |
Collapse
|
10
|
Mohamed RI, Bargal SA, Mekawy AS, El-Shiekh I, Tuncbag N, Ahmed AS, Badr E, Elserafy M. The overexpression of DNA repair genes in invasive ductal and lobular breast carcinomas: Insights on individual variations and precision medicine. PLoS One 2021; 16:e0247837. [PMID: 33662042 PMCID: PMC7932549 DOI: 10.1371/journal.pone.0247837] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 02/14/2021] [Indexed: 12/22/2022] Open
Abstract
In the era of precision medicine, analyzing the transcriptomic profile of patients is essential to tailor the appropriate therapy. In this study, we explored transcriptional differences between two invasive breast cancer subtypes; infiltrating ductal carcinoma (IDC) and lobular carcinoma (LC) using RNA-Seq data deposited in the TCGA-BRCA project. We revealed 3854 differentially expressed genes between normal ductal tissues and IDC. In addition, IDC to LC comparison resulted in 663 differentially expressed genes. We then focused on DNA repair genes because of their known effects on patients' response to therapy and resistance. We here report that 36 DNA repair genes are overexpressed in a significant number of both IDC and LC patients' samples. Despite the upregulation in a significant number of samples, we observed a noticeable variation in the expression levels of the repair genes across patients of the same cancer subtype. The same trend is valid for the expression of miRNAs, where remarkable variations between patients' samples of the same cancer subtype are also observed. These individual variations could lie behind the differential response of patients to treatment. The future of cancer diagnostics and therapy will inevitably depend on high-throughput genomic and transcriptomic data analysis. However, we propose that performing analysis on individual patients rather than a big set of patients' samples will be necessary to ensure that the best treatment is determined, and therapy resistance is reduced.
Collapse
Affiliation(s)
- Ruwaa I. Mohamed
- Center for Informatics Sciences (CIS), Nile University, Giza, Egypt
| | - Salma A. Bargal
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
| | - Asmaa S. Mekawy
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
- University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt
| | - Iman El-Shiekh
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
- University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt
| | - Nurcan Tuncbag
- Graduate School of Informatics, Department of Health Informatics, Middle East Technical University, Ankara, Turkey
| | - Alaa S. Ahmed
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
- University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt
| | - Eman Badr
- University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt
- Faculty of Computers and Artificial Intelligence, Cairo University, Giza, Egypt
- * E-mail: (EB); (ME)
| | - Menattallah Elserafy
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
- University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt
- * E-mail: (EB); (ME)
| |
Collapse
|
11
|
Chan SH, Ni Y, Li ST, Teo JX, Ishak NDB, Lim WK, Ngeow J. Spectrum of Germline Mutations Within Fanconi Anemia–Associated Genes Across Populations of Varying Ancestry. JNCI Cancer Spectr 2021; 5:6146409. [DOI: 10.1093/jncics/pkaa117] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 11/24/2020] [Accepted: 12/16/2020] [Indexed: 12/12/2022] Open
Abstract
Abstract
Background
Fanconi anemia (FA) is a rare genetic disorder associated with hematological disorders and solid tumor predisposition. Owing to phenotypic heterogeneity, some patients remain undetected until adulthood, usually following cancer diagnoses. The uneven prevalence of FA cases with different underlying FA gene mutations worldwide suggests variable genetic distribution across populations. Here, we aim to assess the genetic spectrum of FA-associated genes across populations of varying ancestries and explore potential genotype–phenotype associations in cancer.
Methods
Carrier frequency and variant spectrum of potentially pathogenic germline variants in 17 FA genes (excluding BRCA1/FANCS, BRCA2/FANCD1, BRIP1/FANCJ, PALB2/FANCN, RAD51C/FANCO) were evaluated in 3523 Singaporeans and 7 populations encompassing Asian, European, African, and admixed ancestries from the Genome Aggregation Database. Germline and somatic variants of 17 FA genes in 7 cancer cohorts from The Cancer Genome Atlas were assessed to explore genotype–phenotype associations.
Results
Germline variants in FANCA were consistently more frequent in all populations. Similar trends in carrier frequency and variant spectrum were detected in Singaporeans and East Asians, both distinct from other ancestry groups, particularly in the lack of recurrent variants. Our exploration of The Cancer Genome Atlas dataset suggested higher germline and somatic mutation burden between FANCA and FANCC with head and neck and lung squamous cell carcinomas as well as FANCI and SLX4/FANCP with uterine cancer, but the analysis was insufficiently powered to detect any statistical significance.
Conclusion
Our findings highlight the diverse genetic spectrum of FA-associated genes across populations of varying ancestries, emphasizing the need to include all known FA-related genes for accurate molecular diagnosis of FA.
Collapse
Affiliation(s)
- Sock Hoai Chan
- Division of Medical Oncology, National Cancer Centre Singapore, Cancer Genetics Service, Singapore
| | - Ying Ni
- Genomic Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Shao-Tzu Li
- Division of Medical Oncology, National Cancer Centre Singapore, Cancer Genetics Service, Singapore
| | - Jing Xian Teo
- SingHealth Duke-NUS Institute of Precision Medicine, Singapore
| | - Nur Diana Binte Ishak
- Division of Medical Oncology, National Cancer Centre Singapore, Cancer Genetics Service, Singapore
| | - Weng Khong Lim
- SingHealth Duke-NUS Institute of Precision Medicine, Singapore
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School Singapore, Singapore
- SingHealth Duke-NUS Genomic Medicine Centre, Singapore
| | - Joanne Ngeow
- Division of Medical Oncology, National Cancer Centre Singapore, Cancer Genetics Service, Singapore
- Oncology Academic Clinical Program, Duke-NUS Medical School, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, Singapore
| |
Collapse
|
12
|
Exploring the Role of Mutations in Fanconi Anemia Genes in Hereditary Cancer Patients. Cancers (Basel) 2020; 12:cancers12040829. [PMID: 32235514 PMCID: PMC7226125 DOI: 10.3390/cancers12040829] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 03/23/2020] [Accepted: 03/25/2020] [Indexed: 12/19/2022] Open
Abstract
Fanconi anemia (FA) is caused by biallelic mutations in FA genes. Monoallelic mutations in five of these genes (BRCA1, BRCA2, PALB2, BRIP1 and RAD51C) increase the susceptibility to breast/ovarian cancer and are used in clinical diagnostics as bona-fide hereditary cancer genes. Increasing evidence suggests that monoallelic mutations in other FA genes could predispose to tumor development, especially breast cancer. The objective of this study is to assess the mutational spectrum of 14 additional FA genes (FANCA, FANCB, FANCC, FANCD2, FANCE, FANCF, FANCG, FANCI, FANCL, FANCM, FANCP, FANCQ, FANCR and FANCU) in a cohort of hereditary cancer patients, to compare with local cancer-free controls as well as GnomAD. A total of 1021 hereditary cancer patients and 194 controls were analyzed using our next generation custom sequencing panel. We identified 35 pathogenic variants in eight genes. A significant association with the risk of breast cancer/breast and ovarian cancer was found for carriers of FANCA mutations (odds ratio (OR) = 3.14 95% confidence interval (CI) 1.4–6.17, p = 0.003). Two patients with early-onset cancer showed a pathogenic FA variant in addition to another germline mutation, suggesting a modifier role for FA variants. Our results encourage a comprehensive analysis of FA genes in larger studies to better assess their role in cancer risk.
Collapse
|